K1000 Scheduled Patching is not working

I am having an issue with the K1000 Patch Schedualing. When I schedual patches (Java, Flash, Quicktime) to happen early in the morning they come back as completed but nothing was patched. When I click "run now" the patching works fine and everything is correctly patched. I am running software version:

5.3.45497

This just started happening to us about a week ago, I checked and all the current patches are downloaded to our box. any ideas on what to look for or what could be causing this issue?